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- PDB-5v87: Crystal structure of LARP1-unique domain DM15 bound to m7GpppC -

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Basic information

Entry
Database: PDB / ID: 5v87
TitleCrystal structure of LARP1-unique domain DM15 bound to m7GpppC
ComponentsLa-related protein 1
KeywordsRNA BINDING PROTEIN / Cap-binding / RNA-binding / DM15 / 5'TOP
Function / homology
Function and homology information


cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling ...cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling / positive regulation of macroautophagy / positive regulation of translational initiation / ribosomal small subunit binding / positive regulation of viral genome replication / translation initiation factor binding / negative regulation of translational initiation / positive regulation of translation / mRNA 3'-UTR binding / translational initiation / mRNA 5'-UTR binding / cytoplasmic stress granule / cell population proliferation / negative regulation of translation / cadherin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DM15 / LARP1 HEAT repeat region / Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-91P / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / La-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.692 Å
AuthorsBerman, A.J. / Lahr, R.M.
CitationJournal: Elife / Year: 2017
Title: La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs.
Authors: Lahr, R.M. / Fonseca, B.D. / Ciotti, G.E. / Al-Ashtal, H.A. / Jia, J.J. / Niklaus, M.R. / Blagden, S.P. / Alain, T. / Berman, A.J.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: La-related protein 1
B: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5354
Polymers39,2332
Non-polymers1,3032
Water4,035224
1
A: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1562
Polymers19,6161
Non-polymers5391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3802
Polymers19,6161
Non-polymers7631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.959, 59.962, 60.321
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein La-related protein 1 / La ribonucleoprotein domain family member 1


Mass: 19616.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6PKG0
#2: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#3: Chemical ChemComp-91P / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate / dinucleotide triphosphate cap analog m7GpppC


Mass: 763.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N8O18P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 4,000 (#25 Index-116)

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. obs: 34328 / % possible obs: 92.2 % / Redundancy: 3.4 % / Net I/σ(I): 19.85

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
Cootmodel building
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0V

5c0v


Resolution: 1.692→24.986 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.09
RfactorNum. reflection% reflection
Rfree0.2035 1970 5.74 %
Rwork0.1815 --
obs0.1828 34328 91.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.692→24.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 82 224 2835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082710
X-RAY DIFFRACTIONf_angle_d0.8843649
X-RAY DIFFRACTIONf_dihedral_angle_d11.5131556
X-RAY DIFFRACTIONf_chiral_restr0.045345
X-RAY DIFFRACTIONf_plane_restr0.005455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6916-1.73390.2561440.22522360X-RAY DIFFRACTION94
1.7339-1.78070.20871490.20312463X-RAY DIFFRACTION97
1.7807-1.83310.21711500.18762458X-RAY DIFFRACTION98
1.8331-1.89230.23271470.19352390X-RAY DIFFRACTION95
1.8923-1.95990.22771330.19912222X-RAY DIFFRACTION88
1.9599-2.03830.2041500.18232462X-RAY DIFFRACTION99
2.0383-2.1310.20811540.18462537X-RAY DIFFRACTION99
2.131-2.24330.21811180.18671902X-RAY DIFFRACTION75
2.2433-2.38380.20711190.1761951X-RAY DIFFRACTION77
2.3838-2.56770.20671540.18662521X-RAY DIFFRACTION100
2.5677-2.82570.19731530.18682539X-RAY DIFFRACTION100
2.8257-3.23390.20551540.18072528X-RAY DIFFRACTION99
3.2339-4.07150.1968960.16941580X-RAY DIFFRACTION62
4.0715-24.98830.18551490.17222445X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6932-2.5081-1.60781.49770.92140.56780.31131.3683-0.59660.25940.5743-0.90060.2450.64630.36140.42660.1193-0.03790.7226-0.27180.595216.40081.0255-10.9074
23.620.78292.23583.89321.40334.43610.00410.22180.07410.2765-0.0316-0.38410.06660.53730.08610.1650.0034-0.00980.24380.04760.199710.7149.7165-3.1509
32.77260.48310.50265.6368-0.73293.70010.0266-0.06490.06190.2923-0.0588-0.05050.0449-0.02070.01860.1674-0.0056-0.0040.1354-0.0050.12560.06349.0836-0.6704
46.29952.92621.3197.59813.00076.77520.11020.2205-0.2371-0.2549-0.0695-0.11170.18330.0105-0.0210.13470.028-0.00850.14490.00620.1275-3.38936.9654-10.8925
54.7704-1.10481.4892.4092-2.43682.49620.1226-0.3531-0.2810.12120.0920.31980.0273-0.273-0.22330.1709-0.02310.00480.25890.02050.1854-11.99956.5203-5.1178
63.64772.63021.48254.48653.73625.3424-0.05370.2952-0.1145-0.39850.0964-0.00620.0512-0.1499-0.00690.14810.0051-0.00390.19540.01780.1691-11.397311.0043-14.8739
78.7053-3.0137-2.52373.32313.49627.7364-0.09180.14920.1207-0.14920.05080.80360.2019-0.5434-0.00480.2278-0.0564-0.01090.43440.05990.396-20.24036.8703-11.3202
88.76750.49895.00473.03881.74223.57110.21390.2974-1.4995-0.1797-0.58151.14540.2377-1.38550.4450.42960.0058-0.03570.5649-0.01140.6446-23.597420.629-29.0533
96.1922-0.87991.0623.20854.05235.91180.74161.3714-0.4491-1.6674-0.79820.15770.84470.360.04060.66290.1528-0.10930.525-0.00360.3125-18.642622.3191-37.4961
104.7202-0.22711.98932.88942.73438.1502-0.1843-0.01480.5053-0.1699-0.05190.2615-0.855-0.62170.23890.36530.1081-0.05720.31040.03560.3754-20.529632.8806-22.7735
116.3686-2.8948-3.44733.50361.47713.4203-0.07460.13720.25260.02570.091-0.02260.0592-0.0833-0.00560.23970.02-0.07260.1950.01950.2115-13.120125.4969-21.8085
122.741-0.32130.43783.06830.07015.6169-0.04290.31910.4619-0.11840.011-0.0726-0.32530.24320.02170.2157-0.0294-0.02270.24630.08340.2625-4.935627.4116-23.0485
130.3696-0.0663-0.63482.0918-0.90231.5906-0.04250.70320.4765-0.1004-0.2015-0.2484-0.43950.2106-0.16590.2811-0.0788-0.00660.53650.21950.35156.061427.8969-24.4426
144.97660.9121-1.11835.92092.65195.29930.05750.7231-0.1213-0.0793-0.0903-0.48870.4260.26360.02840.17180.04010.020.32910.06550.21565.835417.6329-20.9875
157.19466.31064.12588.23243.58332.3667-0.05221.37230.5953-0.3835-0.3399-0.12030.53090.78960.39850.55310.12920.19690.91220.21420.515712.753922.7842-30.1745
161.5458-0.171-0.86731.2835-0.03270.67680.028-0.1961-0.0397-0.0268-0.1611-0.49120.01150.2737-0.13870.2768-0.12160.03290.79970.22330.503715.947522.8223-18.5757
173.2286-0.78610.20290.2871-0.34940.95320.14540.01790.3241-0.2040.3164-0.4826-0.4211.2726-0.34770.4026-0.1397-0.00850.8373-0.05751.380714.79610.2914-16.4278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 794 through 809 )
2X-RAY DIFFRACTION2chain 'A' and (resid 810 through 847 )
3X-RAY DIFFRACTION3chain 'A' and (resid 848 through 871 )
4X-RAY DIFFRACTION4chain 'A' and (resid 872 through 887 )
5X-RAY DIFFRACTION5chain 'A' and (resid 888 through 906 )
6X-RAY DIFFRACTION6chain 'A' and (resid 907 through 922 )
7X-RAY DIFFRACTION7chain 'A' and (resid 923 through 941 )
8X-RAY DIFFRACTION8chain 'B' and (resid 794 through 803 )
9X-RAY DIFFRACTION9chain 'B' and (resid 804 through 809 )
10X-RAY DIFFRACTION10chain 'B' and (resid 810 through 827 )
11X-RAY DIFFRACTION11chain 'B' and (resid 828 through 847 )
12X-RAY DIFFRACTION12chain 'B' and (resid 848 through 887 )
13X-RAY DIFFRACTION13chain 'B' and (resid 888 through 906 )
14X-RAY DIFFRACTION14chain 'B' and (resid 907 through 922 )
15X-RAY DIFFRACTION15chain 'B' and (resid 923 through 931 )
16X-RAY DIFFRACTION16chain 'B' and (resid 932 through 940 )
17X-RAY DIFFRACTION17chain 'B' and (resid 941 through 944 )

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